Geonames seems to have modern place names (e.g. Trecwn for the parish in Pembrokeshire, Wales that used to be Llanfair Nant Y Gof until the 1940s). But historical records mostly refer to Llanfair Nant y Gof (FamilySearch has Llanfairnantygof). Are you intending to handle historical place names (Brave!) or ar eyou going to leave it as an exercise for the user to identify the correct modern/historical place name correlation, which might be the pragmatic solution?
We plan on handling historical names too. Geonames won't be the only data set we end up using, it just worked great for getting a prototype running.
The reason that only 60% of WeRelate's places have GIS data is because the other 40% were found only in the Family History Library Catalog (FHLC), not in the Getty TGN or Wikipedia. Those 40% are valuable because they are linked to sources in the FHLC, which seems like it would be useful for your application. The WeRelate place database is the only database I'm aware of that includes the places in the FHLC.